arXiv Computation and Language
The paper introduces Clinical Intent Extraction (CIE), a task that transforms fragmented clinical action annotations into complete structured records called Clinical Intent Representation (CIR). CIR decomposes each action into verb, type, coded target, timing, condition, request‑intent (aligned to HL7 FHIR) and modality, adding dimensions absent in prior datasets. By re‑expressing five heterogeneous corpora into CIR, the authors create CIRCA, a benchmark of 10,011 harmonized intents with human‑validated subsets, crosswalks, and a deterministic FHIR R4 mapper, and demonstrate that existing models perform poorly on the full task, highlighting the need for targeted development.
The paper introduces a retrieval‑augmented multi‑agent framework that automatically generates instance‑specific evaluation rubrics for medical language models. By retrieving authoritative medical evidence, decomposing it into atomic facts, and combining these with user interaction constraints, the system produces fine‑grained criteria that outperform GPT‑4o on HealthBench and LLMEval‑Med. The generated rubrics also guide response refinement, improving medical LLM output quality by 9.2%.
By Yinzhu Chen, Abdine Maiga, Hossein A. Rahmani, Emine Yilmaz
arXiv:2606. 05970v1 Announce Type: cross Abstract: Large language models are increasingly used for structured extraction from clinical free-text notes, but the sensitivity of their output to upstream configuration choices is less understood than their accuracy on fixed benchmarks.
By Martin Murin
arXiv:2606. 12569v1 Announce Type: cross Abstract: We present EDEN (Emergency Department Electronic Notes), a new and unique large-scale corpus of clinical notes produced in Emergency Departments of Italian hospitals.
By Tiziano Labruna, Guido Bertolini, Pietro Ferrazzi, Bernardo Magnini
arXiv:2605.11533v4 Announce Type: replace
Abstract: Routine clinical check-up reports combine laboratory measurements, physiological assessments, imaging findings and visually structured information,...
By Sike Xiang, Shuang Chen, Kevin Qinghong Lin, Jialin Yu, Yijia Sun, Philip Torr, Amir Atapour-Abarghouei
arXiv:2606. 12569v3 Announce Type: replace-cross Abstract: We present eCREAM-MedCorpus, a new and unique large-scale dataset of clinical notes produced in Emergency Departments of Italian hospitals.
By Tiziano Labruna, Guido Bertolini, Pietro Ferrazzi, Bernardo Magnini
arXiv:2606. 12569v2 Announce Type: replace-cross Abstract: We present eCream-MedCorpus, a new and unique large-scale dataset of clinical notes produced in Emergency Departments of Italian hospitals.
By Tiziano Labruna, Guido Bertolini, Pietro Ferrazzi, Bernardo Magnini
arXiv:2508. 14817v2 Announce Type: replace-cross Abstract: Objective: To evaluate whether retrieval-augmented generation (RAG) can serve as an efficient alternative to long-context prompting for clinical reasoning over electronic health records (EHRs).
By Skatje Myers, Dmitriy Dligach, Timothy A. Miller, Samantha Barr, James Landefeld, Yanjun Gao, Matthew Churpek, Anoop Mayampurath, Majid Afshar
arXiv:2606. 24102v1 Announce Type: cross Abstract: Most electronic health record (EHR) foundation models encode clinical events as discrete event tokens from a fixed vocabulary and therefore cannot directly represent events containing unseen concepts or new combinations of concepts and attributes such as numeric values.
By Lin Lawrence Guo, Adam Paul Yan, Emily Vettese, Lillian Sung
The paper identifies a new problem in clinical natural language processing called the clinical lost‑in‑the‑middle (CLitM) effect, where large language models perform poorly on information located near the center of long electronic health record (EHR) documents. Using the MedAlign dataset, the authors quantify a 21.9‑percentage‑point accuracy gap across 2,196 instruction‑response pairs and six models, showing that most critical facts lie in the CLitM trough. They propose Query‑Conditioned Clinical Suppression (QCCS), a lightweight context‑selection gate that outperforms traditional retrieval methods (BM25, dense retrieval, cross‑encoder reranking) on a held‑out set of 83 instructions, achieving up to 25.3% accuracy for middle‑position queries.
whyItMatters":"The study demonstrates that standard retrieval strategies fail to reliably surface central clinical information, and that a query‑aligned selection mechanism can substantially improve model performance on critical EHR data."
By Sanjay Basu
arXiv:2508. 16674v2 Announce Type: replace-cross Abstract: Medical report understanding from real-world document images is essential for generating patient-facing explanations and enabling structured information exchange in clinical systems.
By Fangxin Shang, Yuan Xia, Dalu Yang, Yahui Wang, Binglin Yang
INTERVenE introduces Transformer models that use a knowledge‑based temporal abstraction (KBTA) token stream of named clinical concepts instead of raw measurements, enabling per‑token attributions to resolve directly to clinical concepts. Two variants are offered: an auto‑regressive decoder that generates future abstraction trajectories with step‑wise risk readouts, and a bidirectional encoder that jointly predicts risk and time‑to‑event in a single pass. On 57,078 MIMIC‑IV admissions, the encoder variant outperforms neural baselines with a support‑weighted AUPRC of 0.672 and AUROC of 0.901, while the decoder provides complementary token‑level risk trajectories.
By Shahar Oded, Yuval Shahar
arXiv:2609.12884v1 Announce Type: new
Abstract: A medical claim's correctness often depends not on the claim alone, but on the clinical structure around it. A claim may require a lab reference range,...
By Hasan Iqbal, Sarfraz Ahmad, Hyunjae Kim, Sihyeon Park, Junjie Liao, Qingyu Chen, Preslav Nakov, Yuxia Wang